Exemplo n.º 1
0
  /**
   * Add into to a hash
   *
   * @param hits
   * @param marker
   * @param hit2add
   * @param showGeneDetails
   * @param compareTemplate
   */
  void regionsAddHit(
      HashSet<String> hits,
      Marker hit2add,
      Marker marker,
      boolean showGeneDetails,
      boolean compareTemplate) {
    String hitStr = hit2add.getClass().getSimpleName();

    if (compareTemplate) {
      Gene gene = (Gene) hit2add.findParent(Gene.class);
      if (gene != null)
        hitStr +=
            (hit2add.isStrandPlus() == marker.isStrandPlus())
                ? "_TEMPLATE_STRAND"
                : "_NON_TEMPLATE_STRAND";
    }

    if (showGeneDetails && (hit2add instanceof Gene)) {
      Gene gene = (Gene) hit2add;
      hitStr +=
          "["
              + gene.getBioType()
              + ", "
              + gene.getGeneName()
              + ", "
              + (gene.isProteinCoding() ? "protein" : "not-protein")
              + "]";
    }

    hits.add(hitStr); // Add marker name to the list
  }
  /**
   * Count number of bases, for a given chromosome and marker type
   *
   * @param mtype
   * @param chr
   * @param markers
   * @return
   */
  void countBases(String mtype, Chromosome chr, Markers markers) {
    String chrName = chr.getChromosomeName();
    if (verbose) System.err.print(" " + chrName);

    // Initialize
    byte busy[] = new byte[chr.size()];
    for (int i = 0; i < busy.length; i++) busy[i] = 0;

    for (Marker m : markers) {
      // Same marker type & same chromo? Count bases
      if (m.getChromosomeName().equals(chrName) && markerTypes.isType(m, mtype)) {
        for (int i = m.getStart(); i <= m.getEnd(); i++) busy[i] = 1;
      }
    }

    int latest = 0;
    for (int i = 0; i < busy.length; i++) {
      // Transition? Count another marker
      if ((i > 0) && (busy[i] != 0) && (busy[i - 1] == 0)) {
        if ((i - latest) <= readLength)
          countBases.inc(mtype, i - latest); // Intervals are less than one read away? Unify them
        else countMarkers.inc(mtype);
      }

      // Base busy? Count another base
      if (busy[i] != 0) {
        countBases.inc(mtype);
        latest = i;
      }
    }
  }
Exemplo n.º 3
0
  /**
   * Predict the effect of a seqChange
   *
   * @param seqChange : Sequence change
   * @param seqChangeRef : Before analyzing results, we have to change markers using seqChangerRef
   *     to create a new reference 'on the fly'
   */
  public ChangeEffects seqChangeEffect(Variant seqChange, Variant seqChangeRef) {
    ChangeEffects changeEffects = new ChangeEffects(seqChange, seqChangeRef);

    // ---
    // Chromosome missing?
    // ---
    if (Config.get().isErrorOnMissingChromo() && isChromosomeMissing(seqChange)) {
      changeEffects.addErrorWarning(ErrorWarningType.ERROR_CHROMOSOME_NOT_FOUND);
      return changeEffects;
    }

    // ---
    // Check that this is not a huge deletion.
    // Huge deletions would crash the rest of the algorithm, so we need to stop them here.
    // ---
    if (seqChange.isDel() && (seqChange.size() > HUGE_DELETION_SIZE_THRESHOLD)) {
      // Get chromosome
      String chromoName = seqChange.getChromosomeName();
      Chromosome chr = genome.getChromosome(chromoName);

      if (chr.size() > 0) {
        double ratio = seqChange.size() / ((double) chr.size());
        if (ratio > HUGE_DELETION_RATIO_THRESHOLD) {
          changeEffects.add(chr, EffectType.CHROMOSOME_LARGE_DELETION, "");
          return changeEffects;
        }
      }
    }

    // ---
    // Query interval tree: Which intervals does seqChange intersect?
    // ---
    Markers intersects = query(seqChange);

    // Show all results
    boolean hitChromo = false, hitSomething = false;
    if (intersects.size() > 0) {
      for (Marker marker : intersects) {
        if (marker instanceof Chromosome) hitChromo = true; // Do we hit any chromosome?
        else { // Analyze all markers
          marker.seqChangeEffect(seqChange, changeEffects, seqChangeRef);
          hitSomething = true;
        }
      }
    }

    // Any errors or intergenic (i.e. did not hit any gene)
    if (!hitChromo) {
      if (Config.get().isErrorChromoHit())
        changeEffects.addErrorWarning(ErrorWarningType.ERROR_OUT_OF_CHROMOSOME_RANGE);
    } else if (!hitSomething) {
      if (Config.get().isOnlyRegulation()) changeEffects.setEffectType(EffectType.NONE);
      else changeEffects.setEffectType(EffectType.INTERGENIC);
    }

    return changeEffects;
  }
Exemplo n.º 4
0
  /**
   * Find the last position where a nonsense mediated decay is supposed to occurr This is 50 bases
   * (MND_BASES_BEFORE_LAST_JUNCTION bases) before the last exon-exon junction.
   *
   * @param tr
   * @return
   */
  public int lastNmdPos(Transcript tr) {
    // ---
    // Get last exon
    // ---
    int cdsEnd = tr.getCdsEnd();
    int cdsStart = tr.getCdsStart();
    Marker cds =
        new Marker(
            tr.getChromosome(),
            Math.min(cdsStart, cdsEnd),
            Math.max(cdsStart, cdsEnd),
            tr.getStrand(),
            ""); // Create a cds marker
    Exon lastExon = null;
    int countCodingExons = 0;
    for (Exon exon : tr.sortedStrand()) {
      if (exon.intersects(cdsEnd)) lastExon = exon;
      if (cds.intersects(exon)) countCodingExons++;
    }

    // Only one coding exon? => No NMD
    // Note: I'm assuming that we should have a splice event in a coding part of the transcript for
    // NMD to happen.
    if (countCodingExons <= 1) return -1;

    // Sanity check
    if (lastExon == null)
      throw new RuntimeException(
          "Cannot find last coding exon for transcript '"
              + tr.getId()
              + "' (cdsEnd: "
              + cdsEnd
              + ")\n\t"
              + tr);

    // ---
    // Find that position of MND_BASES_BEFORE_LAST_JUNCTION before the last exon-exon junction
    // ---
    int lastExonJunction = tr.isStrandPlus() ? lastExon.getStart() : lastExon.getEnd();
    int chrPos[] = tr.baseNumberCds2Pos();
    int lastNmdPos = -1;
    for (int cdsi = chrPos.length - 1; cdsi >= 0; cdsi--) {
      if (chrPos[cdsi] == lastExonJunction) {
        if (cdsi > MND_BASES_BEFORE_LAST_JUNCTION)
          lastNmdPos = chrPos[cdsi - MND_BASES_BEFORE_LAST_JUNCTION - 1];
        else return tr.isStrandPlus() ? 0 : Integer.MAX_VALUE; // Out of CDS range
        return lastNmdPos;
      }
    }

    throw new RuntimeException(
        "Cannot find last exon junction position for transcript '" + tr.getId() + "'\n\t" + tr);
    // return -1;
  }
  /** Count bases covered for each marker type */
  public void countBases() {
    // ---
    // Add all markers
    // ---
    Markers markers = new Markers();
    markers.add(snpEffectPredictor.getMarkers());
    for (Gene gene : snpEffectPredictor.getGenome().getGenes()) {
      markers.add(gene);
      markers.add(gene.markers());
    }

    for (Chromosome chr : snpEffectPredictor.getGenome()) markers.add(chr);

    // ---
    // Calculate raw counts
    // ---
    for (Marker m : markers) {
      String mtype = markerTypes.getType(m);
      String msubtype = markerTypes.getSubType(m);

      rawCountMarkers.inc(mtype);
      rawCountBases.inc(mtype, m.size());

      // Count sub-types (if any)
      if (msubtype != null) {
        rawCountMarkers.inc(msubtype);
        rawCountBases.inc(msubtype, m.size());
      }
    }

    // ---
    // Count number of bases for each marker type (overlap and join)
    // ---
    for (String mtype : rawCountMarkers.keysSorted()) {
      if (mtype.equals(Chromosome.class.getSimpleName()))
        continue; // We calculate chromosomes later (it's faster)

      if (verbose) System.err.print(mtype + ":");

      if (countMarkers.get(mtype) == 0) {
        for (Chromosome chr : snpEffectPredictor.getGenome()) countBases(mtype, chr, markers);
      }

      if (verbose) System.err.println("");
    }

    // Show chromosomes length
    String mtype = Chromosome.class.getSimpleName();
    for (Chromosome chr : snpEffectPredictor.getGenome()) {
      countBases.inc(mtype, chr.size());
      countMarkers.inc(mtype);
    }
  }
Exemplo n.º 6
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 public Gene getGene() {
   if (marker != null) {
     if (marker instanceof Gene) return (Gene) marker;
     return (Gene) marker.findParent(Gene.class);
   }
   return null;
 }
Exemplo n.º 7
0
 /** Get intron (if any) */
 public Intron getIntron() {
   if (marker != null) {
     if (marker instanceof Intron) return (Intron) marker;
     return (Intron) marker.findParent(Intron.class);
   }
   return null;
 }
Exemplo n.º 8
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 public Transcript getTranscript() {
   if (marker != null) {
     if (marker instanceof Transcript) return (Transcript) marker;
     return (Transcript) marker.findParent(Transcript.class);
   }
   return null;
 }
Exemplo n.º 9
0
 /** Get exon (if any) */
 public Exon getExon() {
   if (marker != null) {
     if (marker instanceof Exon) return (Exon) marker;
     return (Exon) marker.findParent(Exon.class);
   }
   return null;
 }
Exemplo n.º 10
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  /**
   * Is this deletion a LOF?
   *
   * <p>Criteria: 1) First (coding) exon deleted 2) More than 50% of coding sequence deleted
   *
   * @param changeEffect
   * @return
   */
  protected boolean isLofDeletion(ChangeEffect changeEffect) {
    Transcript tr = changeEffect.getTranscript();
    if (tr == null)
      throw new RuntimeException("Transcript not found for change:\n\t" + changeEffect);

    // ---
    // Criteria:
    // 		1) First (coding) exon deleted
    // ---
    if (changeEffect.getEffectType() == EffectType.EXON_DELETED) {
      Variant seqChange = changeEffect.getSeqChange();
      if (seqChange == null)
        throw new RuntimeException("Cannot retrieve 'seqChange' from EXON_DELETED effect!");
      if (seqChange.includes(tr.getFirstCodingExon())) return true;
    }

    // ---
    // Criteria:
    // 		2) More than 50% of coding sequence deleted
    // ---

    // Find coding part of the transcript (i.e. no UTRs)
    Variant seqChange = changeEffect.getSeqChange();
    int cdsStart = tr.isStrandPlus() ? tr.getCdsStart() : tr.getCdsEnd();
    int cdsEnd = tr.isStrandPlus() ? tr.getCdsEnd() : tr.getCdsStart();
    Marker coding = new Marker(seqChange.getChromosome(), cdsStart, cdsEnd, 1, "");

    // Create an interval intersecting the CDS and the deletion
    int start = Math.max(cdsStart, seqChange.getStart());
    int end = Math.min(cdsEnd, seqChange.getEnd());
    if (start >= end) return false; // No intersections with coding part of the exon? => not LOF
    Marker codingDeleted = new Marker(seqChange.getChromosome(), start, end, 1, "");

    // Count:
    //   - number of coding bases deleted
    //   - number of coding bases
    int codingBasesDeleted = 0, codingBases = 0;
    for (Exon exon : tr) {
      codingBasesDeleted += codingDeleted.intersectSize(exon);
      codingBases += coding.intersectSize(exon);
    }

    // More than a threshold? => It is a LOF
    double percDeleted = codingBasesDeleted / ((double) codingBases);
    return (percDeleted > deleteProteinCodingBases);
  }
Exemplo n.º 11
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  /**
   * Is the chromosome missing in this marker?
   *
   * @param marker
   * @return
   */
  boolean isChromosomeMissing(Marker marker) {
    // Missing chromosome in marker?
    if (marker.getChromosome() == null) return true;

    // Missing chromosome in genome?
    String chrName = marker.getChromosomeName();
    Chromosome chr = genome.getChromosome(chrName);
    if (chr == null) return true;

    // Chromosome length is 1 or less?
    if (chr.size() < 1) return true;

    // Tree not found in interval forest?
    if (!intervalForest.hasTree(chrName)) return true;

    // OK, we have the chromosome
    return false;
  }
Exemplo n.º 12
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  /** Save nextprot markers */
  void save() {
    String nextProtBinFile = config.getDirDataVersion() + "/nextProt.bin";
    if (verbose) Timer.showStdErr("Saving database to file '" + nextProtBinFile + "'");

    // Add chromosomes
    HashSet<Chromosome> chromos = new HashSet<Chromosome>();
    for (Marker m : markers) chromos.add(m.getChromosome());

    // Create a set of all markers to be saved
    Markers markersToSave = new Markers();
    markersToSave.add(genome);
    for (Chromosome chr : chromos) markersToSave.add(chr);
    for (Marker m : markers) markersToSave.add(m);

    // Save
    MarkerSerializer markerSerializer = new MarkerSerializer();
    markerSerializer.save(nextProtBinFile, markersToSave);
  }
Exemplo n.º 13
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  /** Set values for codons around change. */
  public void setCodonsAround(String codonsLeft, String codonsRight) {
    codonsAroundOld =
        codonsLeft.toLowerCase() + codonsRef.toUpperCase() + codonsRight.toLowerCase();
    codonsAroundNew =
        codonsLeft.toLowerCase() + codonsAlt.toUpperCase() + codonsRight.toLowerCase();

    // Amino acids surrounding the ones changed
    CodonTable codonTable = marker.codonTable();
    String aasLeft = codonTable.aa(codonsLeft);
    String aasRigt = codonTable.aa(codonsRight);
    aasAroundOld = aasLeft.toLowerCase() + aaRef.toUpperCase() + aasRigt.toLowerCase();
    aasAroundNew = aasLeft.toLowerCase() + aaAlt.toUpperCase() + aasRigt.toLowerCase();
  }
Exemplo n.º 14
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  /** Return functional class of this effect (i.e. NONSENSE, MISSENSE, SILENT or NONE) */
  public FunctionalClass getFunctionalClass() {
    if (variant.isSnp()) {
      if (!aaAlt.equals(aaRef)) {
        CodonTable codonTable = marker.codonTable();
        if (codonTable.isStop(codonsAlt)) return FunctionalClass.NONSENSE;

        return FunctionalClass.MISSENSE;
      }
      if (!codonsAlt.equals(codonsRef)) return FunctionalClass.SILENT;
    }

    return FunctionalClass.NONE;
  }
Exemplo n.º 15
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  /**
   * Find closest gene to this marker
   *
   * <p>In case more than one 'closest' gene is found (e.g. two or more genes at the same distance).
   * The following rules apply:
   *
   * <p>i) If many genes have the same 'closest distance', coding genes are preferred.
   *
   * <p>ii) If more than one coding gene has the same 'closet distance', a random gene is returned.
   *
   * @param inputInterval
   */
  public Gene queryClosestGene(Marker inputInterval) {
    int initialExtension = 1000;

    String chrName = inputInterval.getChromosomeName();
    Chromosome chr = genome.getChromosome(chrName);
    if (chr == null) return null;

    if (chr.size() > 0) {
      // Extend interval to capture 'close' genes
      for (int extend = initialExtension; extend < chr.size(); extend *= 2) {
        int start = Math.max(inputInterval.getStart() - extend, 0);
        int end = inputInterval.getEnd() + extend;
        Marker extended = new Marker(chr, start, end, 1, "");

        // Find all genes that intersect with the interval
        Markers markers = query(extended);
        Markers genes = new Markers();
        int minDist = Integer.MAX_VALUE;
        for (Marker m : markers) {
          if (m instanceof Gene) {
            int dist = m.distance(inputInterval);
            if (dist < minDist) {
              genes.add(m);
              minDist = dist;
            }
          }
        }

        // Found something?
        if (genes.size() > 0) {
          // Find a gene having distance 'minDist'. Prefer coding genes
          Gene minDistGene = null;

          for (Marker m : genes) {
            int dist = m.distance(inputInterval);
            if (dist == minDist) {
              Gene gene = (Gene) m;
              if (minDistGene == null) minDistGene = gene;
              else if (!minDistGene.isProteinCoding() && gene.isProteinCoding()) minDistGene = gene;
            }
          }

          return minDistGene;
        }
      }
    }

    // Nothing found
    return null;
  }
Exemplo n.º 16
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  /** Set codon change. Calculate effect type based on codon changes (for SNPs & MNPs) */
  public void setCodons(String codonsOld, String codonsNew, int codonNum, int codonIndex) {
    codonsRef = codonsOld;
    codonsAlt = codonsNew;
    this.codonNum = codonNum;
    this.codonIndex = codonIndex;

    CodonTable codonTable = marker.codonTable();

    // Calculate amino acids
    if (codonsOld.isEmpty()) aaRef = "";
    else {
      aaRef = codonTable.aa(codonsOld);
      codonDegeneracy = codonTable.degenerate(codonsOld, codonIndex); // Calculate codon degeneracy
    }

    if (codonsNew.isEmpty()) aaAlt = "";
    else aaAlt = codonTable.aa(codonsNew);
  }
Exemplo n.º 17
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  /** Show a string with overall effect */
  public String effect(
      boolean shortFormat, boolean showAaChange, boolean showBioType, boolean useSeqOntology) {
    String e = "";
    String codonEffect = codonEffect(showAaChange, showBioType, useSeqOntology); // Codon effect

    // Create effect string
    if (!codonEffect.isEmpty()) e = codonEffect;
    else if (isRegulation())
      return getEffectTypeString(useSeqOntology) + "[" + ((Regulation) marker).getName() + "]";
    else if (isNextProt())
      return getEffectTypeString(useSeqOntology)
          + "["
          + VcfEffect.vcfEffSafe(((NextProt) marker).getId())
          + "]"; // Make sure this 'id' is not dangerous in a VCF 'EFF' field
    else if (isMotif())
      return getEffectTypeString(useSeqOntology)
          + "["
          + ((Motif) marker).getPwmId()
          + ":"
          + ((Motif) marker).getPwmName()
          + "]";
    else if (isCustom()) {
      // Custom interval
      String label = ((Custom) marker).getLabel();
      double score = ((Custom) marker).getScore();
      if (!Double.isNaN(score)) label = label + ":" + score;
      if (!label.isEmpty()) label = "[" + label + "]";
      return getEffectTypeString(useSeqOntology) + label;
    } else if (isIntergenic() || isIntron() || isSpliceSite())
      e = getEffectTypeString(useSeqOntology);
    else if (!message.isEmpty()) e = getEffectTypeString(useSeqOntology) + ": " + message;
    else if (marker == null)
      e =
          getEffectTypeString(
              useSeqOntology); // There are cases when no marker is associated (e.g. "Out of
                               // chromosome", "No such chromosome", etc.)
    else e = getEffectTypeString(useSeqOntology) + ": " + marker.getId();

    if (shortFormat) e = e.split(":")[0];

    return e;
  }
Exemplo n.º 18
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  /**
   * Name of the regions hit by a marker
   *
   * @param marker
   * @param showGeneDetails
   * @param compareTemplate
   * @param id : Only use genes or transcripts matching this ID
   * @return
   */
  public Set<String> regions(
      Marker marker, boolean showGeneDetails, boolean compareTemplate, String id) {
    if (Config.get().isErrorOnMissingChromo() && isChromosomeMissing(marker))
      throw new RuntimeEOFException("Chromosome missing for marker: " + marker);

    boolean hitChromo = false;
    HashSet<String> hits = new HashSet<String>();

    Markers intersects = query(marker);
    if (intersects.size() > 0) {
      for (Marker markerInt : intersects) {

        if (markerInt instanceof Chromosome) {
          hitChromo = true; // OK (we have to hit a chromosome, otherwise it's an error
          hits.add(markerInt.getClass().getSimpleName()); // Add marker name to the list
        } else if (markerInt instanceof Gene) {
          // Analyze Genes
          Gene gene = (Gene) markerInt;
          regionsAddHit(hits, gene, marker, showGeneDetails, compareTemplate);

          // For all transcripts...
          for (Transcript tr : gene) {
            if ((id == null)
                || gene.getId().equals(id)
                || tr.getId().equals(id)) { // Mathes ID? (...or no ID to match)

              // Does it intersect this transcript?
              if (tr.intersects(marker)) {
                regionsAddHit(hits, tr, marker, showGeneDetails, compareTemplate);

                // Does it intersect a UTR?
                for (Utr utr : tr.getUtrs())
                  if (utr.intersects(marker))
                    regionsAddHit(hits, utr, marker, showGeneDetails, compareTemplate);

                // Does it intersect an exon?
                for (Exon ex : tr)
                  if (ex.intersects(marker))
                    regionsAddHit(hits, ex, marker, showGeneDetails, compareTemplate);

                // Does it intersect an intron?
                for (Intron intron : tr.introns())
                  if (intron.intersects(marker))
                    regionsAddHit(hits, intron, marker, showGeneDetails, compareTemplate);
              }
            }
          }
        } else {
          // No ID to match?
          if (id == null) regionsAddHit(hits, markerInt, marker, showGeneDetails, compareTemplate);
          else {
            // Is ID from transcript?
            Transcript tr = (Transcript) markerInt.findParent(Transcript.class);
            if ((tr != null) && (tr.getId().equals(id))) {
              regionsAddHit(
                  hits,
                  markerInt,
                  marker,
                  showGeneDetails,
                  compareTemplate); // Transcript ID matches => count
            } else {
              // Is ID from gene?
              Gene gene = (Gene) markerInt.findParent(Gene.class);
              if ((gene != null) && (gene.getId().equals(id)))
                regionsAddHit(
                    hits,
                    markerInt,
                    marker,
                    showGeneDetails,
                    compareTemplate); // Gene ID matches => count
            }
          }
        }
      }
    }

    if (!hitChromo) throw new RuntimeException("ERROR: Out of chromosome range. " + marker);
    return hits;
  }
Exemplo n.º 19
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  /** Show annotations counters in a table */
  void analyzeSequenceConservation() {
    if (verbose)
      Timer.showStdErr(
          "Sequence conservation analysis." //
              + "\n\tAA sequence length  : "
              + 1 //
              + "\n\tMin AA count        : "
              + HIGHLY_CONSERVED_AA_COUNT //
              + "\n\tMin AA conservation : "
              + HIGHLY_CONSERVED_AA_PERCENT //
          );

    ArrayList<String> keys = new ArrayList<String>();
    keys.addAll(countAaSequenceByType.keySet());
    Collections.sort(keys);

    // Show title
    StringBuilder title = new StringBuilder();
    for (char aa : GprSeq.AMINO_ACIDS) title.append(aa + "\t");
    title.append("\t" + title);
    if (verbose)
      System.out.println(
          "Amino acid regions:\n\tTotal\tMax count\tAvg len\tConservation\tCatergory\tControlled Vocabulary\t"
              + title
              + "\tOther AA sequences:");

    // Show AA counts for each 'key'
    for (String key : keys) {
      long seqLen = 0, totalSeqs = 0, maxCount = 0;
      CountByType cbt = countAaSequenceByType.get(key);
      long total = cbt.sum();

      boolean highlyConservedAaSequence = false;

      StringBuilder sb = new StringBuilder();

      // For each single amino acid "sequence"
      for (char aa : GprSeq.AMINO_ACIDS) {
        long count = cbt.get("" + aa);
        if (count > 0) {
          seqLen += 1 * count;
          totalSeqs += count;
          maxCount = Math.max(maxCount, count);

          sb.append(count);
          double perc = ((double) count) / total;

          // We estimate that if most AA are the same, then changing this AA can cause a high impact
          // in protein coding
          if ((perc > HIGHLY_CONSERVED_AA_PERCENT) && (total >= HIGHLY_CONSERVED_AA_COUNT))
            highlyConservedAaSequence = true;
        }
        sb.append("\t");
      }

      // Sequences of more than one AA
      for (String aas : cbt.keySet()) {
        long count = cbt.get(aas);
        double perc = ((double) count) / total;
        if (aas.length() > 1) {
          seqLen += aas.length() * count;
          totalSeqs += count;
          maxCount = Math.max(maxCount, count);

          sb.append(String.format("\t" + aas + ":" + count));
          if ((perc > HIGHLY_CONSERVED_AA_PERCENT) && (total >= HIGHLY_CONSERVED_AA_COUNT))
            highlyConservedAaSequence = true;
        }
      }

      long avgLen = seqLen / totalSeqs;

      // Show line
      if (verbose)
        System.out.println( //
            "\t"
                + total //
                + "\t"
                + maxCount //
                + "\t"
                + avgLen //
                + "\t"
                + (highlyConservedAaSequence ? "High" : "") //
                + "\t"
                + key //
                + "\t"
                + sb //
            );

      // Mark highly conserved
      if (highlyConservedAaSequence) {
        int count = 0;
        for (Marker m : markers) {
          NextProt nextProt = (NextProt) m;
          if (m.getId().equals(key)) {
            nextProt.setHighlyConservedAaSequence(true);
            count++;
          }
        }

        if (verbose)
          Timer.showStdErr(
              "NextProt "
                  + count
                  + " markers type '"
                  + key
                  + "' marked as highly conserved AA sequence");
      }
    }
  }
Exemplo n.º 20
0
  public String toString(boolean useSeqOntology, boolean useHgvs) {
    // Get data to show
    String geneId = "", geneName = "", bioType = "", transcriptId = "", exonId = "", customId = "";
    int exonRank = -1;

    if (marker != null) {
      // Gene Id, name and biotype
      Gene gene = getGene();
      Transcript tr = getTranscript();

      // CDS size info
      if (gene != null) {
        geneId = gene.getId();
        geneName = gene.getGeneName();
        bioType = getBiotype();
      }

      // Update trId
      if (tr != null) transcriptId = tr.getId();

      // Exon rank information
      Exon exon = getExon();
      if (exon != null) {
        exonId = exon.getId();
        exonRank = exon.getRank();
      }

      // Regulation
      if (isRegulation()) bioType = ((Regulation) marker).getCellType();
    }

    // Add seqChage's ID
    if (!variant.getId().isEmpty()) customId += variant.getId();

    // Add custom markers
    if ((marker != null) && (marker instanceof Custom))
      customId += (customId.isEmpty() ? "" : ";") + marker.getId();

    // CDS length
    int cdsSize = getCdsLength();

    String errWarn = error + (error.isEmpty() ? "" : "|") + warning;

    String aaChange = "";
    if (useHgvs) aaChange = getHgvs();
    else aaChange = ((aaRef.length() + aaAlt.length()) > 0 ? aaRef + "/" + aaAlt : "");

    return errWarn //
        + "\t"
        + geneId //
        + "\t"
        + geneName //
        + "\t"
        + bioType //
        + "\t"
        + transcriptId //
        + "\t"
        + exonId //
        + "\t"
        + (exonRank >= 0 ? exonRank : "") //
        + "\t"
        + effect(false, false, false, useSeqOntology) //
        + "\t"
        + aaChange //
        + "\t"
        + ((codonsRef.length() + codonsAlt.length()) > 0 ? codonsRef + "/" + codonsAlt : "") //
        + "\t"
        + (codonNum >= 0 ? (codonNum + 1) : "") //
        + "\t"
        + (codonDegeneracy >= 0 ? codonDegeneracy + "" : "") //
        + "\t"
        + (cdsSize >= 0 ? cdsSize : "") //
        + "\t"
        + (codonsAroundOld.length() > 0 ? codonsAroundOld + " / " + codonsAroundNew : "") //
        + "\t"
        + (aasAroundOld.length() > 0 ? aasAroundOld + " / " + aasAroundNew : "") //
        + "\t"
        + customId //
    ;
  }